Transcriptional regulation of gene expression, its timing, tissue distribution and response to both[unreadable] internal and environmental inputs, is a key link between the genome and phenotype. Variation in expression[unreadable] patterns across cell types is a primary determinant of tissue identity and function. Individual genetic variation in[unreadable] gene expression determines both our susceptibility to disease and provides the substrate for evolutionary[unreadable] adaptation. An integrated view of genome dynamics requires understanding these relationships in terms of[unreadable] genome organization. Toward this goal we will:[unreadable] Aim 3a. analyze publicly available gene expression data resources for physical correlates of tissue-specific[unreadable] gene expression patterns and for clustering of co-expression in LD domains and networks.[unreadable] Aim 3b. survey gene expression in 16 mouse strains using microarrays. The selected strains will include[unreadable] 'classical' inbred strains, inbred strains derived from M.m. musculus, M.m. domesticus, and M.m. castaneus[unreadable] origin, and inbred strains derived from hybrid origins. We will examine four tissues in mice of both sexes and[unreadable] relate our findings to genome organization and functional variation.[unreadable] Aim 3c. develop statistical methods and software for these analyses.